dolfin team mailing list archive

[Marie Rognes <meg@xxxxxxxxxxx>]

Jed Brown wrote:
> On Wed 2008-08-20 17:35, Marie Rognes wrote:
>   
> > Matthew Knepley wrote:
> >     
> > > On Wed, Aug 20, 2008 at 5:08 AM, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
> > >   
> > >       
> > > > Marie Rognes wrote:
> > > >     
> > > >         
> > > > > Garth N. Wells wrote:
> > > > >       
> > > > >           
> > > > > > Marie Rognes wrote:
> > > > > >         
> > > > > >             
> > > > > > > I'm trying to compile dolfin with PETSc and SLEPc, but without MPI:
> > > > > > >
> > > > > > >      ./scons.local enableMpi=no withPetscDir=$PETSC_DIR
> > > > > > >     withSlepcDir=$SLEPC_DIR
> > > > > > >
> > > > > > > This gives the following error:
> > > > > > >
> > > > > > >           
> > > > > > >               
> > > > > > Hopefully this is fixed now, although my PETSc is built with MPI, so I
> > > > > > can't be sure. Let me know if it's ok or otherwise.
> > > > > >         
> > > > > >             
> > > > > I get through the compilation stage now, so that's good :)
> > > > >
> > > > > However, if I try to "import dolfin", I get:
> > > > >
> > > > >        Python 2.5.2 (r252:60911, Jun 19 2008, 15:12:17)
> > > > >    [GCC 4.1.2 (Gentoo 4.1.2 p1.0.2)] on linux2
> > > > >    Type "help", "copyright", "credits" or "license" for more information.
> > > > >     >>> import dolfin
> > > > >    Traceback (most recent call last):
> > > > >      File "<stdin>", line 1, in <module>
> > > > >      File
> > > > >
> > > > > "/home/meg/src/dolfin/dolfin/local/lib/python2.5/site-packages/dolfin/__init__.py",
> > > > >
> > > > >    line 13, in <module>
> > > > >        from assemble import *
> > > > >      File
> > > > >
> > > > > "/home/meg/src/dolfin/dolfin/local/lib/python2.5/site-packages/dolfin/assemble.py",
> > > > >
> > > > >    line 22, in <module>
> > > > >        from dolfin import *
> > > > >      File
> > > > >
> > > > > "/home/meg/src/dolfin/dolfin/local/lib/python2.5/site-packages/dolfin/dolfin.py",
> > > > >
> > > > >    line 7, in <module>
> > > > >        import _dolfin
> > > > >    ImportError: /home/meg/src/dolfin/dolfin/local/lib/libdolfin.so:
> > > > >    undefined symbol: MPIUNI_TMP
> > > > >
> > > > >       
> > > > >           
> > > > Looks like a linking problem to PETSc. Can you compile C++ DOLFIN programs?
> > > >     
> > > >         
> > >   
> > >       
> > Nope. The cpp poisson demo gives:
> >
> > meg in cpp >> scons
> > scons: Reading SConscript files ...
> > scons: done reading SConscript files.
> > scons: Building targets ...
> > c++ -o main.o -c -Wall -pipe -ansi -g -Werror -O2 -fno-strict-aliasing 
> > -pthread -DDEBUG -DNDEBUG -DPACKAGE_VERSION="0.8.0" -DHAS_PETSC=1 
> > -DHAS_SLEPC=1 -DHAS_UMFPACK=1 -DHAS_GTS=1 
> > -I/home/meg/src/dolfin/dolfin/local/include 
> > -I/usr/lib/python2.5/site-packages/numpy/core/include 
> > -I/home/meg/src/slepc -I/home/meg/src/slepc/include 
> > -I/usr/include/python2.5 -I/home/meg/src/petsc/bmake/linux-gnu-c-debug 
> > -I/home/meg/src/petsc/include 
> > -I/home/meg/src/petsc-2.3.3-p13/include/mpiuni -I/usr/include/libxml2 
> > -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include main.cpp
> > c++ -o demo -Wl,-rpath,/home/meg/src/slepc/lib/linux-gnu-c-debug 
> > -Wl,-rpath,/home/meg/src/petsc/lib/linux-gnu-c-debug -pthread 
> > -Wl,--export-dynamic main.o -L/home/meg/src/dolfin/dolfin/local/lib 
> > -L/home/meg/src/slepc/lib/linux-gnu-c-debug -L/usr/lib/atlas 
> > -L/home/meg/src/petsc/lib/linux-gnu-c-debug -ldolfin -lslepc -lblas 
> > -lumfpack -lamd -lgts -lxml2 -lpetscts -lpetscsnes -lpetscksp -lpetscdm 
> > -lpetscmat -lpetscvec -lpetsc -lgthread-2.0 -lrt -lgmodule-2.0 -ldl 
> > -lglib-2.0
> > /home/meg/src/dolfin/dolfin/local/lib/libdolfin.so: undefined reference 
> > to `Petsc_MPI_Abort'
> >
> >     
> > > Almost  certainly it is an incomplete link line when libdolfin.so is
> > > constructed. When PETSc
> > > is built without MPI, it creates an extra library (libmpiuni) which
> > > must be linked against to
> > > get these symbols.
> > >   
> > >       
> > I'm not quite sure what that implies... But, I should somehow add 
> > -lmpiuni when linking dolfin? For instance in the pkgconfig file scons 
> > creates for petsc?
> >     
>
> What does the it look like when you build a PETSc demo?  What should be
> on the `Libs:' line of petsc.pc is the result of the following:
>
> echo -e 'include ${PETSC_DIR}/bmake/common/base\nlink:\n\t-@echo ${PETSC_LIB}' | make PETSC_DIR=~/usr/petsc-2* PETSC_ARCH=ompic-opt -f - link
>
> It will probably be ugly and often has lots of repetition for no
> apparent reason.  However, it should be reliable.
>   


Hurray! My DOLFIN is back among the living. (Now, I just need to get it 
to understand that SLEPc is hanging around as well.)

Just adding -lmpiuni to petsc.pc did not help. Adding the output of

   echo -e 'include ${PETSC_DIR}/bmake/common/base\nlink:\n\t-@echo 
${PETSC_LIB}' |     make -f - link
  
did. Thanks a lot!

However, there should probably be a prettier way of doing this?

--
Marie E. Rognes
Ph.D Fellow, 
Centre of Mathematics for Applications, 
University of Oslo
http://folk.uio.no/meg